Monday, June 10, 2019

Behe Rides Again

The Science Magazine blog has a specific subsection for book reviews. The comment traffic was very low until the recent review of the Intelligent Design Creationist book, "Darwin Devolves" by Michael Behe.  The review was authored by Nathan H. Lents, S. Joshua Swamidass, and Richard E. Lenski. Over the last few weeks there were 170 comments posted on the review page itself.

The Intelligent Design Creationist movement, IDC, got its public start with Phillip Johnson's 1993 book "Darwin on Trial" (Downers Grove, IL: InterVarsity Press). It was really inspired by the 1987 US Supreme Court ruling in Edwards v. Aguillard, where the Court held Louisiana's "Creationism Act" as unconstitutional. This meant that "special creation," and "creationists," and  were not terms that would pass for "science" in public schools. Consequently, they were replaced with Intelligent Design, and "intelligent design proponents" in a creationist book eventually sold as a high school biology textbook, "Of Pandas and People" (1989, Foundation for Thought and Ethics). This was the true origin of ID creationism.

The "science" of ID creationism got its first play in a 1996 book by Michael Behe, "Darwin's Black Box," where he argued that life manifested a property he called, "irreducible complexity." Further Behe insisted that irreducible complexity could not have come to be by material evolutionary means.

Behe had to eat his denials when under oath during the 2005 "Pandas Trial" over the Dover PA attempt to teach ID creationism as science.

My favorite part of Behe's collapse was;

Kitzmiller v. Dover: Day 12, PM: Michael Behe (continued)
Q. Let's discuss archaeology a little bit more. Matt, if you could pull up Exhibit 722? May I approach, Your Honor?
THE COURT: You may.
Q. And Professor Behe, this is a chapter from a book called Why Intelligent Design Failed: A Scientific Critique of the New Creationism. Do you see that?
A. Yes, I do.
Q. We're going to look at chapter 8 of that book, if you could pull up the chapter heading there? And it's titled The Explanatory Filter, Archaeology and Forensics, and it's written by somebody named Gary S. Hurd. Are you familiar with Dr. Hurd?
A. No, I am not.

Tuesday, May 07, 2019

James Tour, Liar for Jesus

The blog post I did a few days ago, "James Tour: The Mystery of the Origin of Life" resulted in a YouTube video with Bill Ludlow.

It has gone 'live' this morning.

"Gary Hurd And Bill Ludlow Respond To James Tour's Mystery Of Life"

I must insist that I am not as old as I look. The camera added at least 20 years, and I have a mirror to prove it!

If you have visited this page from the Disco'tute website, Go Read The Original Piece.

Wednesday, May 01, 2019

Boiled Creationist with a Side of Hexaglycine;

Sarfati on Imai et al. (1999)

Gary S. Hurd, Ph.D.
This was a piece I wrote 17 years ago for the Australian web journal "No Answers in Genesis."

In an Answers in Genesis web article titled "Hydrothermal origin of life?" Jonathan Sarfati manages to write three pages about a single five page original peer reviewed paper "Elongation of Oligopeptides in a Simulated Submarine Hydrothermal System" published in the magazine Science by Imai et al. (1999), and to make over seventeen errors of fact, emphasis or interpretation. What is sad is that it will take a longer paper than either of the preceding to point out the errors made by Sarfati.  This is why very few scientists would bother to reply. Not bad, even for a fanatical creationist. Sarfati titles his piece, 'Hydrothermal origin of life?' but it barely speaks to this topic at all, since he excludes most of the existing literature. For the convenience of the reader we will follow the same headings as used by Sarfati.
Abstract and Introduction 

Let us start with the first sentence in Sarfati's abstract -
'Some Japanese researchers have claimed to prove that life could have arisen in a submarine hydrothermal vent'.
Two errors and one questionable word use in just one short sentence! First, not all of the research group were from Japan. Second, nowhere in the refereed article Imai et al. (1999) was there the assertion that their paper proved that life originated in hydrothermal environments [one of the research team did make a similar statement in a newspaper interview given to Elaine Lies of Reuters news service, but more on that later]. And one must wonder why Sarfati was so insistent on the presumed ethnicity of the research team, so much so that he overlooked that André Brack is French. I could have overlooked this had Sarfati not reiterated that the researchers were non-westerners in his fourth paragraph which he opens with -
'Five researchers in Nagaoka, Japan, claimed to have simulated such conditions in a flow reactor'.
Again we see that Sarfati presses his concern with ethnicity and continues the pejorative use of the word 'claimed'. I would say to anyone who might seek to defend Sarfati by pointing out that the research was conducted in Japan, why then did Sarfati not say, 'An international team of scientists working in Japan...'? In the same pejorative manner, Sarfati continues to use quotation marks in what can only be a rhetorical effort to detract from the content of the Imai et al. (1999) paper.
The last sentence in Sarfati's abstract is -
'High temperatures would degrade any complex molecules over the alleged geological time.'
While it is possible that Sarfati could be referring to Lazcano and Miller (1996), who estimated that the existence of hydrothermal systems in the early Archean could limit the time available for the origin of life to approximately a ten million year interval, Sarfati is clearly not referring to Imai et al. (1999). There is no sense that 'alleged geological time' is invoked by the refereed paper, but the fact that the Imai et al. (1999) paper is clear evidence that this was not the case and that Lazcano and Miller must also modify their position, should be obvious to even a naive reader. So just for openers we can reject Sarfati as a careful or competent reader. Before we are off the first page, barely beyond his abstract, we see that Sarfati cannot read the list of authors, or their professional affiliations, rhetorically uses pejorative language, and fails to understand the basic facts of the article under his examination. The news release Sarfati later quotes also clearly identified Brack as French, precluding the defence that Sarfati was confused by other sources.
Sarfati offers us an unintended bit of humor in just the second sentence of his article:
' ...such an organism could barely repair DNA damage, could no longer fine-tune the ability of its remaining genes, would lack the ability to digest complex compounds, and would need a comprehensive supply of organic nutrients in its environment.'
What strikes me as amusing is that, apart from the fact that DNA is not considered a likely feature of the first organisms (Nelson et al. 2000, Nesbit and Sleep 2001) and that the phrase 'could no longer fine-tune the ability of its remaining genes' is nonsensical, this is an excellent description of the theoretical first organisms which are proposed to be very simple Chemohetrotrophs (Lazcano and Miller 1996, Dyall and Johnson 2000). I think we can score this as two and a half errors.
In Sarfati's second paragraph he invents a new kind of energy, 'undirected' energy, which he informs us is destructive rather than constructive. One must assume that in whatever Universe Sarfati belongs there is some sort of directed energy that is purely constructive.  Our universe has energy, only energy, and at the molecular level under discussion it is neither directed or otherwise.  In the case of hydrothermal systems energy is expressed as heat and pressure.
Pressure is an important feature of the reaction kinetics of hydrothermal systems, a point that Sarfati omits in either a purposeful or an incompetent manner in the third sentence of the second paragraph -
'The idea is that the heat can help synthesize polymers...'.
Energy in the form of heat in the absence of high pressure will indeed prove to be largely destructive. [1]
Hydrothermal Vents

The second section of Sarfati's paper is titled, 'Hydrothermal Vents'. I think it is obvious to anyone familiar with the origin of life (OOL) research literature that a single, four page article can hardly contain the 'Hydrothermal origin of life', and can at best add or subtract a tiny feature of the growing theoretical edifice of hydrothermal vents and OOL literature. For those who are familiar with this area of science, it is enough to note that Sarfati fails to refer to any of G. Wachershauser's papers (or those he has co-authored), or those by E. L. Shock and his colleagues, on the hydrothermal system contributions to the origin of life, to realize that Sarfati's title is at least incompetent. [2] Sarfati fails to add any conditions to hydrothermal vents that could justify his use of the word 'claimed' as in 'Five researchers in Nagaoka, Japan, "claimed" to have simulated such conditions in a flow reactor.' This is notably the primary reference to Imai et al. (1999). 

What follows is Sarfati's very incomplete three sentence summery of the Imai et al. (1999) experimental procedure and anyone who is interested in the actual experiment or its results will need to read the original paper.

Experimental Results

Sarfati's five sentence presentation of the Imai et al. (1999) results is as ill informed as his understanding of their experimental method. The first sentence merely informs us that Sarfati thinks the 'most spectacular results' were the production of tetraglycine and hexaglycine in the presence of CuCl2. Sarfati is completely wrong when he states that 'The Cu+2 ions catalyzed the formation of tetraglycine... '. The actual scientists note:
'The presence of copper ions seems to have prevented the hydrolysis of tetraglycine. The tetraglycine therefore reentered the reaction region and further reacted with a glycine, producing a diglycine, a triglycine, or a diketopiperazine molecule when the amount of tetraglycine becomes sufficient.'
This is significant because Sarfati continues his misrepresentation of the experiment's results by noting that -
'...the product with the highest yield was the cyclic dimer, diketopiperazine, which peaked at about 1% yield, then dropped.'
What really happened was that about five minutes into the experiment which produced hexaglycine, diketopipazine peaked at about 1% and was about to begin to be consumed by the production of hexaglycine. From about five to nine minutes into the experiment, sharp drops in the amounts of diketopipazine and diglycine are observed at the same time as hexaglycine is first detectable. The amount of reactants naturally continues to decline as they are consumed in the production of the larger molecules, particularly hexaglycine.  At the end of the data collection period reported, thirty minutes, there is so little remaining glycine that the reaction is effectively halted. Had the researchers continuously supplied additional glycine, I'm certain that, based on the chemistry involved, there would have been continued production of the observed oligopeptides. 

This is far, far different from the results as misrepresented by Sarfati. In fact nowhere does Sarfati even mention the experimental results under the nonacidified conditions. I score this as four errors of fact or interpretation.

Sarfati's Assessment

Koichiro Matsuno gave an interview to Elaine Lies of the Reuters News Service on the occasion of the publication of the Science article. In that article, Matsuno gives the quote reproduced by Sarfati:
'Man has been asking "what is life" for thousands of years. But the real question is where did life begin,' Matsuno told reporters. 'For 10 years, underwater hydrothermal vents have been thought to be the place where life began and we were able to prove it.'
The entire Reuters article is available here.

Sarfati asked if this statement was justified by the results reported in Imai et al. (1999) and his answer was, 'No!'

Our answer as well is no, for reasons that I will return to later, but without the exclamation mark. This might surprise some readers, but no, Matsuno has not proven where life originated. Now, it will come as no surprise that this is virtually the only point of agreement I have with Sarfati's diatribe.  For example, Sarfati thinks that Matsuno is speaking -
' ...based on evolutionary faith... '
which is merely an attempt by Sarfati to falsely portray science as a 'religion'.’ A simple explanation for Matsuno's enthusiasm, based on my personal experiences with scientists, is that lab bench scientists and theoreticians typically exaggerate the significance of their work in the popular press as it facilitates (they imagine) their future funding prospects. Another contributing factor is that one really can't get away with that kind of grandstanding in the scientific literature, as scientific reviewers, unlike news reporters, are selected for their relevant expertise in a given area. And so, the opportunity to wildly expand the scope and significance of one's research under the questioning and encouragement of a reporter can be overwhelming.   Finally, Matsuno, a physicist, may truly feel that his statement is correct in the light of his research. The exact boundary between complex chemistry and the origin of life is after all more philosophical than physical. 

Sarfati offers the reasons that he rejects Matsuno's grand claim of discovery under four bullet points. These are a predictable mishmash of misunderstood science and selective quotes.

1)  Sarfati thinks he knows what the concentration of glycine was on the prebiotic Earth, and eventually offers an out of date (1984, re-issued in 1992) reference to a creationist work in his support. The cited reference, and Sarfati, are oblivious to different mechanisms of abiogenic amino acid synthesis and concentration that have been demonstrated since 1984. These mechanisms are mentioned in Imai et al. (1999). A fairly extensive reference list is given in their footnote #5, and so were available to Sarfati. Additionally, Sarfati's use of the obsolete estimate of glycine concentration is directly contradicted by Amend and Shock (1998) also referenced by Imai et al. (1999).  As a further observation, we note that the reaction mechanism demonstrated by Imai et al. (1999), is based on the recycling of reactants in the hydrothermal system. Under these conditions the absolute concentration of reactants is less critical than the number of cycles. By increasing the concentrations of the reactant glycine, Imai et al. (1999) merely minimized the amount of time needed to produce the resulting oligomers. As seen in their results shown in Figures 1and 2, the major reactions took place in less than 30 minutes by which time the amount of monomer glycine dropped too low within their closed system to rapidly generate additional product. Nor does Sarfati calculate (or seem aware of) the abiogenic production of glycine produced within the hydrothermal system by mechanisms following from Horita and Berndt (1999). 

Sarfati follows with another complete non sequitur -
'Also, any glycine produced would be subject to oxidative degradation in an oxygenic atmosphere.'
First, there is no issue with the generation of glycine; the abiogenic production of amino acids has been established back to the first spark chamber experiments of Miller (1953) and Miller/Urey (1959), and many additional reaction mechanisms since then as referenced above. Second, there is strong data that the early Earth had a reducing, or minimally, an anoxic atmosphere so that 'oxidative degradation' could not occur (Hunten 1993, Kasting 1993, Kump et al. 2001 among others. For a contrasting opinion see Ohmoto 1997, and for a direct counter argument to Ohmoto see Holland 1999. For a biochemical study see Des Marais 2000, and for some further theoretical considerations see Dismukes, et al. 2001, Lasaga, and Ohmoto 2002). Further, even had there been a merely anoxic atmosphere, and ocean for that matter, reductive reservoirs would be at least as common as they are today in hydrothermal systems. Why, imagine that!  Even today with an Earth oxidised by billions of years of photosynthesis, hydrothermal systems are strongly reducing to neutral. Sarfati suggests in a footnote that the -
'The "strongest evidence" for an anoxic ancient earth atmosphere is that we know chemical evolution took place, and this would have been impossible with oxygen present!'
And he gives two references from the 1970s (one which he did not even read in the original) which use this line of argument, (for a more recent exploration of this reasoning see Hill, 1998).  Oddly, Sarfati calls this a use of circular logic.  There are two points to be made here; first there is ample direct evidence for a reducing to anoxic Hadean and Early Archean which Sarfati must be aware of (the reader need only consult the references offered above) and second, this is not an example of circular logic.  Finally, there is no such thing as an 'oxygenic atmosphere' although one could read Noll et al. 1997 for a discussion of the UV production of ozone on extra-terrestrial ices.  Indeed, this ozone leads us to Sarfati's next blunder. 

Sarfati tries to cover the fact that his 'oxygen the destroyer' story fits science fiction better than science fact with the argument that if the presence of oxygen didn't destroy nascent life on Earth, then the absence of oxygen, in the form of ozone, would. It would seem to be impossible to lose an argument like that wouldn't it? A real 'heads I win, tails you lose' sort of deal. Unfortunately for Sarfati, reality intrudes again. In Noll et al. (1997) for instance it is learned that an atmosphere with less than 10% of the Earth's current oxygen level could have as much as 25% of the Earth's current ozone. Further, without any free oxygen, or ozone, there are several additional means available that could have protected early macromolecules, and life itself. For example, Cleaves and Miller (1998) observe that the prebiotic organic compounds in the oceans would easily absorb the UV radiation flux during the Archean (when the Sun produced less heat [IR radiation] and more UV than today). Earlier, Sagan and Chyba (1997) had shown that methane photolysis could have provided an effective ultraviolet radiation shield for the Earth and prevented, or minimized global glaciation. However, a third model exists, the occasional impact melting of frozen oceans on the early Earth (early to middle Archean approximately 3.9 Ga to 3.5, 1Ga=1 billion years before present) which provides oceanic organic chemical concentration, and an impact heat sink in addition to UV protection of prebiotic chemicals by ice (Bada et al. 1994).   Indeed there is strong evidence that these processes could have begun during the Hadean as early as 4.4 Ga (Sleep and Neuhoff 2001, Wilde et al. 2001).

Still clinging to a feeble argument that low glycine abundance could somehow interfere with oliogomerization, Sarfati introduces ' ...adsorption by clays, precipitation or complexation [sic] by metal ions, or reactions with other organic molecules... ' as available mechanisms that could draw down the available stocks of glycine. This is rather funny. Just what does Sarfati think the products of these steps might be? For instance, the absorption of abiogenic organic molecules on K-feldspars (Parsons et al. 1998), or calcite, which also addresses one feature of the pointless homochirality argument Sarfati will soon turn to (Hazen et al. 2001) have been proposed mechanisms for the abiogenic production of polypeptides leading to the origin of life.  Maybe Sarfati would prefer (Ni,Fe)S complexes which takes us right back into the original hydrothermal literature (Huber and Wachterhauser 1998, etc.). There is a massive literature on the clay montmorillonite and its probable contribution to the origin of life (eg. Ferris and Ertem 1993, Ferris et al. 1996). And the most ludicrous is Sarfati's complaint that glycine would form peptides, or even polymers with 'other organic molecules', when his fourth objection to the Imai et al. (1999) results is that they have only examined the production of oligomers.   I repeat, 'just what does Sarfati think the products of these steps might be?' Sarfati, in trying to deny adequate stocks of glycine to Imai et al. (1999), which we have already seen is irrelevant, has retreated into advocating the proposed origin of life chemical reactions of many other researchers he has attempted to refute elsewhere.  Is this why he has failed to provide these references for this part of his failed attempt to refute Imai et al. (1999)?

2)  Sarfati's next issue with the newspaper statement by Matsuno separates into three parts. Sarfati in his first sentence of this section claims that hydrothermal dynamics would be harmful to 'other vital components of life', even while admitting that the experiment adequately represented the hydrothermal chemistry of glycine. This is complicated. The original authors, Imai, Honda, Hatori, Brack and Matsuno do not go so far, as they explicitly point out some of the ways that their experiment does not reflect realistic Hadean or Archean hydrothermal conditions. Also, Sarfati has changed the field of the discussion by abandoning Imai et al. (1999) to move on to a discussion of RNA and high temperatures. This is an interesting problem which could warrant an extended discussion. But this is not germane to the results of Imai et al. (1999) and would ridiculously extend this already long paper. Second, as if the stability of RNA was not distancing enough, Sarfati also makes a technically irrelevant reference to chirality which makes one erroneous statement and seems to merely provide Sarfati the opportunity to reference himself again. An idle entertainment at a conference is to see who is able to identify the well known cell membrane protein gramicidin A by its structure of alternating L- and D-amino acids (an activity preferably conducted in the conference hotel's bar). Finally, Sarfati wishes us to ignore the results of Imai et al. (1999) because they have not done the experiment that Sarfati judges is 'incomprehensible' to have not been executed. Actually, Sarfati should take this issue up with the funding sources rather than the experimenters. It is worth noting that Imai et al. (1999) reference Amend and Scheck (1998), who's thermodynamic analysis indicates that at least half of the twenty essential amino acids, also the most common, should react similarly to cytosine under the conditions used by Imai et al. (1999).

3)  Sarfati begins this bullet point with an odd sentence, 'The longest polymer (or rather, oligomer) formed was hexaglycine'.  Imai et al. (1999) never refer to any product of their experiment as a polymer. So who is Sarfati correcting? It would seem that Sarfati is correcting Sarfati. Could there be any other reason than appearing erudite that might explain Sarfati creating an error, 'polymer', so that he can correct it '(or rather, oligomer)'? Next, Sarfati compared hexaglycine with the structure of enzymes. Imai et al. (1999) nowhere claim to have produced enzymes, nor do they compare their products to enzymes. Sarfati needs to decide if he is criticizing a newspaper interview, which hardly needs the folderol of a 'research' article, or is he trying to make some response to a peer-reviewed paper in Science? As a response to the paper published in Science, Sarfati's effort is far short of adequate.

4)  By point four, Sarfati is largely repeating himself. Unfortunately he is repeating his own errors. The first sentence allows us to watch Sarfati misapply the term 'homo-oligomer'. The word 'oligomer' means a polymer of up to five units of the same monomer, with the root 'oligo' meaning scant, and by definition monomers are restricted to simple molecules which are the repeating units of a polymer. A 'homo-oligomer' is found where two to many copies of a complex macromolecule polymerize. A web search on 'homo-oligomer' contrasted by a similar search on 'oligomer' will easily return sufficient examples to clarify this to the interested reader, or one can consult a good dictionary. Next, Sarfati incorrectly asserts, 'But life requires many polymers in precise sequences of 20 different types of amino acids'.  Indeed it is the very fact that there is considerable imprecision allowed in living systems that makes evolution possible, and neither is it true that all 20+ amino acids are involved in all polymers associated with life. And next, 'Thus Matsuno's experiments offer not the slightest explanation for the complex, high-information polymers of living organisms'.   Well of course it does, by empirically demonstrating an effective set of reactions which lead to the abiogenic formation of a complex molecule.


Sarfati concludes with an irrelevant quotation which I will ignore. I will conclude with a short explication as to why, in spite of my complete disdain for Sarfati's incompetent treatment of this topic, I agree that Matsuno's newspaper interview statement that, 'For 10 years, underwater hydrothermal vents have been thought to be the place where life began and we were able to prove it', is incorrect, and is not supported by the results in Imai et al. (1999). There is a considerable amount of work on the contribution of marine hydrothermal vent systems to the origin of life, some of which has been referenced in this short paper. Hopefully an interested reader may follow these references to the current thinking in this issue.

But, no one should expect to find a definitive answer to the question, 'Where did life begin?'. For, even if a bench chemist should derive (perhaps I should say create) a set of self replicating molecules which assemble into a cell, they will not have demonstrated how life originated on the planet Earth some three to four billion years ago. Not even should their created cell have characteristics closely similar to some extant Archaea will this demonstrate how life originated or where this event occurred. Such a demonstration, if possible, will lay in the field of paleo-geochemistry. The laboratory studies are of critical importance as they lead us to search for particular chemical and isotopic signals from the past which unless alerted to we might miss. Still, in the final analysis, it is in the rocks that an OOL hypothesis will stand or fall, just as it was geology and paleontology which first provided the scope and physical evidence to sustain evolutionary theory.

[1] This omission of high pressure effects on macromolecule stability is also found in Levy and Miller (1998) which Sarfati uses in support of his attack on Imai et al. (1999). Miller and his colleagues also make the same omission in Lazcano and Miller (1996), and Miller and Lazcano (1995) on theoretical grounds. Miller and his colleagues all wrote prior to Imai et al. (1999) and based their conclusions on either computational methods or limited experimental data. For a properly considered opinion of the relative contributions of pressure and heat to macromolecular stability consult the references in Note #2, particularly Shock (1990). This only increases the significance of empirical studies such as Imai et al. (1999) as theory generally must give way to data. 

[2] Below are some citations for the reader truly interested in research on the geothermal/ hydrothermal origins of life:

Amend, J. P. , E. L. Shock 1998, Blochl et al. 1992, Huber and Wachtershauser 1997, 1998, Shock 1990, Wachtershauser 2000, Zolotov and Shock 1998.  

Amend, J. P. , E. L. Shock 1998, Energetics of Amino Acid Synthesis in Hydrothermal Ecosystems, Volume 281, number 5383, Issue of 11 Sep , pp. 1659-1662.

Bada, Jeffrey. L., C. Bigham, Stanley L. Miller 1994, Impact melting of frozen oceans on the early Earth: Implications for the origin of life, PNAS-USA v.91: 1248-1250.

Blochl, Elisabeth, Martin Keller, Gunter Wachtershauser, Karl Otto Stetter 1992, Reactions depending on iron sulfide and linking geochemistry with biochemistry, PNAS-USA v.89: 8117-8120.

Cleaves, H. James, Stanley L. Miller 1998, Oceanic protection of prebiotic organic compounds from UV radiation, PNAS-USA v. 95, issue 13: 7260-7263.

Des Marais, David J. 2000, When Did Photosynthesis Emerge on Earth?, Science 289 (5485): 1703.

Dismukes, G. C., V. V. Klimov, S. V. Baranov, Yu. N. Kozlov, J. DasGupta, A. Tyryshkin 2001, The Origin of Atmospheric Oxygen on Earth: The Innovation of Oxygenic Photosynthesis, PNAS-USA vl 98 no. 5: 2170-2175.

Ferris, J.P., A.R. Hill, Jr., R. Liu, and L.E. Orgel 1996, Synthesis of long prebiotic oligomers on mineral surfaces, Nature 381: 59-61.

Ferris, J.P., and G. Ertem 1993. Montmorillonite catalysis of RNA oligomer formation in aqueous solution, A model for the prebiotic formation of RNA, J Am Chem Soc 115: 12270-12275.

Hazen, R.M., T.R. Filley, and G.A. Goodfriend 2001, Selective adsorption of L- and D-amino acids on calcite: Implications for biochemical homochirality, Proceedings of the National Academy of Sciences 98 (May 8):5487.

Hill, L.C. Jr., 1998, The 'Urey Hypothesis' Revisited: Molecular Genetics and Contemporary Chronologies. Early Chronology and Planetary Precesses, July 1998 (Abs.)
Holland, Heinrich D. 1999, When did the Earth's atmosphere become oxic? A Reply, The Geochemical News #100: 20-22.

Horita, Juske, Michael E. Berndt 1999, Abiogenic Methane Formation and Isotropic Fractionization Under Hydrothermal Conditions, Science 285 (5430): 1055.

Hunten, Donald M. 1993, Atmospheric Evolution of the Terrestrial Plants, Science 259:915-920.

Huber, Claudia, Gunter Wachtershauser 1997, Activated Acetic Acid by Carbon Fixation on (Fe,Ni)S Under Primordial Conditions, Science v. 276: 245-247.

Huber, Claudia, Gunter Wachtershauser 1998, Peptides by Activation of Amino Acids with CO on (Ni,Fe)S Surfaces: Implications for the Origin of Life, Science v.281: 670-672.
Imai, E., Honda, H., Hatori, K., Brack, A. and Matsuno, K. 1999, Elongation of oligopeptides in a simulated submarine hydrothermal system, Science 283(5403): 831–833.

Kasting, J.F. 1993, Earth's early atmosphere, Science 259: 920-926.

Kump, Lee R., James F. Kasting, Mark E. Barley 2001, Rise of atmospheric oxygen and the 'upside-down' Archean mantle, Geochemistry, Geophysics, Geosystems vol. 2 paper# 2000GC000114. 

Lasaga, A.C. and Ohmoto, H. 2002, The oxygen geochemical cycle: dynamics and stability, Geochimica et Cosmochimica Acta vol 66, #3 361-381.

Lazcano, Antonio, Stanley L. Miller 1996, The Origin and Early Evolution of Life: Prebiotic Chemistry, the Pre-RNA World,and Time, Cell vol 85:793-798.

Levy, M and Miller, S.L., 1998, The stability of the RNA bases: Implications for the origin of life, Proc. Natl. Acad. Sci. USA 95(14):7933–38.

Miller, Stanley L. 1953, A Production of Amino Acids Under Possible Primitive Earth Conditions, Science vol. 117:528-529.

Miller, Stanley, Harold C. Urey 1959, Organic Compound Synthesis on the Primitive Earth, Science vol 139 Num 3370: 254-251.

Miller, S. L., Lazcano, Antonio 1995, The origin of life- did it occur at high temperatures?, J. Mol. Evol. 41:689-682.

Noll KS, Roush TL, Cruikshank DP, Johnson RE, Pendleton YJ. 1997, Detection of ozone on Saturn's satellites Rhea and Dione, Nature, July 3; 388(6637): 45-7.

Ohmoto, H. 1997, When Did the Earth's Atmosphere Become Oxic?, The Geochemical News, 93:
12-13, 26-27.

Parsons, Ian, Martin R. Lee, and Joseph V. Smith 1998, Biochemical Evolution II: Origin of Life in Tubular Microstructures on Weathered Feldspar Surfaces, Proceedings of the National Academy of Science 95 (26): 15173.

Sleep, N. H., K. Zahnle, P. S. Neuhoff 2001, Initiation of clement surface conditions on the earliest Earth, PNAS-USA v.98 No. 7: 3666-3672.

Wachtershauser, Gunter 2000, Perspective, Science v.289 : 1308.
Wilde, Simon A., John W. Valley, William H. Peck, Collin M. Graham 2001, Evidence from detrital zircons for the existence of continental crust and oceans on Earth 4.4 Gyr ago, Nature (letters) Vol 409:175-181.

Zolotov, M. Yu., E. L. Shock 1998, Volcanic Gases: Synthesis of Organic Compounds on the Present and Early Earth, Abstract, 1998 Origin of the Earth and Moon, Dec. Monterey CA.

Monday, April 29, 2019

James Tour: The Mystery of the Origin of Life

James Tour is a professional chemist. His principle work area was synthetic organic chemistry directly focused on building nano machines. He is published, and a tenured professor at Rice University, Texas.

Years ago he experienced a religious conversion and joined the “Jews for Jesus” faction. More recently he also began a second career of giving public lectures denying evolutionary biology, and particularly implying that life cannot exist without supernatural intervention by the Biblical God.

A recent example hosted by the Discovery Institute is a classic of its kind. It is both revealing that the Intelligent Design movement is just plain vanilla creationism, and that James Tour lies his ass off for money, adulation, and I suppose his hopes for salvation. The talk was presented at the 2019 Dallas Science and Faith Conference at Park Cities Baptist Church in Dallas and was sponsored by Discovery Institute’s Center for Science and Culture.

There are too many falsehoods, and misrepresentations to review in detail. However, at about 43 minutes into the video, James Tour starts a rant accusing Harvard University professor, and Nobel Laureate Jack Szostak of lying. The Szostak article that Tour falsely claimed was "part of the primary literature" was a 2 1/2 page sketch published 9 May, 2018. It was not in the main section of Nature magazine, nor was it part of the "primary scientific literature." The Nature website makes this adamantly clear at the end of this short little intro to prebiotic sugar and the origin of life, quote, "This article is part of Innovations In The Biggest Questions In Science, an editorially independent supplement produced with the financial support of third parties."

This popularized, simplified item is just an outline, a sketch from the actual “primary literature.” The lead cartoon of an imaginary molecule hatching a bird sets the tone.

So who is lying?

James Tour shows a slide at 45:20 that was a clip from Szostak's little paper. The molecule structures are presented in a very simple manner. The core atoms are represented as colored dots, Carbon, Nitrogen, Oxygen, and Phosphorus. Hydrogen atoms are not shown, and all chemical bonds between atoms are represented by simple lines. The actual professional publication of this chemical reaction pathway is “Prebiotic synthesis of simple sugars by photoredox systems chemistry”


Highlighting the upper left molecules, Tour shouts, "Those are not sugars!" blah blah "That is fictitious! I don't know of any sugars that have that chemical composition. You don't know that! He is lying to you! That's not real!" 

The truth is that the illustration showed the structure of glyceraldehyde. This is the core of all sugar on Earth. This is undergraduate chemistry. This is the molecular structure James Tour insisted did not exist. This undergraduate level chemistry!

Seriously- undergraduate level chemistry.

Who is lying? 

Moving on we see another undergraduate level chemistry error that Tour made. At 45:58 of his little rant about Szostak, he insisted that there was no cyanide in the illustration above. There isn't any. The graphic clearly states "Cyanide derivatives."

In fact, the structural formulas are of cyanide derivatives. The one on the left is CN2, or cyanonitrene.

On the right is Cyanoethynyl

Create Date: 2005-08-08 

At 46:10 Tour starts to yap that the right most stick drawing is "not a nucleotide." From 46:10 to 46:20 Tour shouts “it is not the right structure, he could have at least used the right structure … “ In fact it is cytosine bound to ribose and the phosphate to the ribose. This is RNA's nucleoside cytidine. It is directly and spontaneously formed in nature from the starting chemistry.  It is the “right structure.”

And again showing the addition of the phosphate;

Above are two excellent graphic presentations that expose the failure of James Tour's grasp of basic biochemistry. They were prepared, and shared to me by the blogger "Evograd"

Who is lying?
There are multiple reaction pathways that would have been supported in the ancient Earth environment. I find that James Tour is badly mistaken.

In fact he is a liar.

The actual primary literature that Szostak used for his sugar origin illustration was “Prebiotic synthesis of simple sugars by photoredox systems chemistry” (Ritson, D. and Sutherland, J.D., 2012 Nature chemistry, 4(11), p.895).

There is in fact a large literature on the prebiotic origin of sugars essential for the origin of life that demonstrates many different reaction pathways. Here is a small sample;

Vázquez-Mayagoitia Á, Horton SR, Sumpter BG, Šponer J, Šponer JE, Fuentes-Cabrera M. 2011 "On the stabilization of ribose by silicate minerals" Astrobiology. 2011 Mar;11(2):115-21. doi:10.1089/ast.2010.0508. 

Weber AL. 1997 "Prebiotic amino acid thioester synthesis: thiol-dependent amino acid synthesis from formose substrates (formaldehyde and glycolaldehyde) and ammonia" Origins of Life and Evolution of the Biosphere 28: 259-270.

Matthew W. Powner, Béatrice Gerland & John D. Sutherland, 2009 "Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions" Nature 459, 239-242 (14 May 2009)

Springsteen G, Joyce GF. 2004 "Selective derivatization and sequestration of ribose from a prebiotic mix" J Am Chem Soc. 2004 Aug 11;126(31):9578-83

Ricardo, A., Carrigan, M. A., Olcott, A. N., Benner, S. A. 2004 "Borate Minerals Stabilize Ribose" Science January 9; 303: 196

It is very important to recognize that this chemistry even happens in outer space as demonstrated by this finding;

Cooper, George, Novelle Kimmich, Warren Belisle, Josh Sarinana, Katrina Brabham, Laurence Garrel 2001 "Carbonaceous meteorites as a source of sugar-related organic compounds for the early Earth" Nature 414, 879 – 883.

From 43:04 to 46:51, James Tour told 9 individual lies (not counting repeats, or what could be charitably attributed to his gross ignorance). 15 lies in under 4 minutes counting repeated lies. That is Trumpian. And, his lies are exposed by undergraduate level chemistry. They are not even sophisticated lies. They are stupid obvious lies.

Edit to add:  In a new development 3 May 2019, James Tour claimed he personally has apologized to Jack Szostak.

Dear Peter, thank you for writing to me. That was a strong word (“lying”) which I regret saying. I have already apologized to Jack Szostak by phone, and he very graciously accepted the apology. If given a chance, I would likewise apologize to any of those cited in that talk to whom I said such a thing. My behavior was inappropriate.

Like many things that I do and say in life, there are elements upon which I have regrets and wish that I had done differently. My life is filled with those occasions. In fact, I can literally claim almost daily I do something or say something which I wish I had not. Those closest to me get the brunt of it, but thankfully they have also been gracious in forgiving me. And for that I am thankful.

“O wretched man that I am! Who shall deliver me from the body of this death? I thank God through Jesus Christ our Lord.” Romans 7:24-25a.

I do not read or write on blogs-- or almost never. So if you wish, you may post this on Peaceful Science, though my words were far from peaceful, to my shame.

God bless,
James Tour

(He did not post this to his YouTube rant slandering Prof. Jack Szostak and others. So, this slander is still ongoing).

Of course there are new questions that are suggested. I learned that at least one person emailed to Szostak about the Disco'tute YouTube. They also included a link to this blog post. Prof. Szostak replied that he would leave a personal message for Prof. Tour.

He said he might send Tour a personal message, but that publicly responding would be pointless because these people don't respond to facts.

The intermediary (They asked to be left anonymous. Why???) sent a similar email to James Tour suggesting he take down the Disco'tute YouTube to avoid "embarrassment," and also included the link. Tour's reaction was far different. He sent emails to the university where the intermediary teaches. His emails were to the Dean of the School of Medicine, and the Uni HRS. Tour accused that I was a stooge of the 'intermediary' and hinted we were merely trying to extort Tour, and the Disco'tute.


Well, things have certainly escalated.  I had also contacted Tour about this issue, and mentioned that your video might be coming out so he should consider getting ahead of the curve and taking down the video to reduce the damage that might be done to his professional reputation.  He has interpreted this as a threat and seems to think I am now the head of some vast conspiracy to extort him.  He has gone so far as to forward my emails to the dean of my department as well as other adminstrators.
What a drama queen.
So, the new questions added to all the others above;

Did Tour really apologize? After all, he lies his ass off for applause lines.
Will Tour post the "new facts" to the YouTube?
Will Tour insist that the creationists take down the Disco'tute video slandering Szostak, and others?

Inquiring minds...